Open image and segmentation collections

The Open Collection Table... command allows users to open a collection table containing references to multiple datasets, facilitating batch visualization. The command supports various viewing and grouping modes and data root configurations.

Command Description

The Open Collection Table... is designed to:

• Open a collection table specified by the user.
• Configure data root paths based on absolute paths or relative paths.
• Support different viewing modes for data visualization.
• Optionally handle access credentials for protected S3 buckets.

Parameters

• Table Path: The file location of the collection table to be opened. The table must be a TAB-separated text file.
• Data Root: Specifies how the data URIs in the table are interpreted:
• PathsInTableAreAbsolute : Assume URIs are absolute paths.
• UseTableFolder : Use the folder containing the table as the root for relative paths.
• UseBelowDataRootFolder : Use a specified folder as the root for relative paths.
• Data Root Folder: Optional. Specify this if paths in the table are relative and you want to use a specific directory as the root.
• Viewing Mode: Determines the visualization mode:
  • ThreeDimensional : Enables arbitrary plane slicing for volumetric viewing.
  • Planar : Restricts browsing to the XY, YZ, or XZ planes.
• S3 Access Key: Optional. Access key for accessing data in a protected S3 bucket.
• S3 Secret Key: Optional. Secret key for accessing data in a protected S3 bucket.

Collection Table Specification

The collection table must adhere to the following specifications, with exact column names given in brackets.

Important notes

• The table must be a TAB-separated text file
  • You can create such a table, e.g., in Excel via “Save As..”, choosing the “File Format” “Tab-delimited Text”.
• Only the uri column must be present; all other columns are optional.
• Please see the JavaDoc for an up-to-date and a more comprehensive description.
• Please see this folder for example tables.

Columns

This list just provides an overview. See the JavaDoc for more details and example entries.

• URI Column (uri): Must contain valid URIs pointing to image or spots datasets. Supported formats include OME-Zarr, BDV XML, ilastik HDF5, Parquet, and others.
• Name Column (name): Optional. Determines the label for data display within MoBIE. If absent, a name is derived from the file name.
• Type Column (type): Optional. Specifies the pixel type (“intensities”, “labels”, “spots”). Defaults to “intensities” if absent or invalid.
• Channel Column (channel): Optional. Zero-based integer Determines which channel of a multi-channel dataset to load. Defaults to channel 0 if absent or invalid.
• Color Column (color): Optional. Specifies the lookup table coloring for intensities. Defaults to “white” if absent or invalid.
• Blend Column (blend): Optional. Determines the blending mode (“sum” or “alpha”). Defaults to “sum” if absent or invalid.
• Affine Column (affine): Optional. Specifies an affine transformation to apply upon display.
• View Column (view): Optional. Determines the view name for access in MoBIE UI. Defaults to the name from the Name column.
• Exclusive Column (exclusive): Optional. Determines if a view is exclusive (“true” or “false”). Defaults to “false”.
• Group Column (group): Optional. Specifies a UI selection group for the view. Defaults to “views” if absent.
• Labels Table Column (labels_table): Optional. Used for “labels” type data, specifies a path to a segmentation table.
• Contrast Limits Column (contrast_limits): Optional. Specifies contrast limits for intensities. Defaults to auto-contrast if absent or invalid.
• Grid Column (grid): Optional. Groups data into a grid view. Defaults to no grid if absent.
• Format Column (format): Optional. Specifies the data format (e.g., OmeZarr). Defaults based on file ending if absent.

Usage

• Provide the path to the collection table and configure the data root as needed.
• Choose the desired viewing mode for data visualization.
• Optionally, provide S3 access credentials if accessing protected data.